Biology: Chapter 2 The Cell: An Overview Cell...
Transcript of Biology: Chapter 2 The Cell: An Overview Cell...
Biology: Chapter 2 The Cell: An Overview
Cell Theory:1) all organisms are comprised of one or more cells2) the cell is the basic structural and functional unit of all living organisms3) cells arise only from the division of preexisting cells
2.1Cells:
carry out the essential processes of life contain highly organized systems of molecules (nucleic acids, DNA, RNA, etc) use chemical molecules or light as energy sources respond to changes in their external environment by altering their internal
reactions cells duplicate & pass on hereditary info some unicellular à yeasts, fungi, amoebas, some protists some multicellular à plants & animals individual cells of multicellular organisms are potentially capable of surviving by
themselves if placed in a chemical medium that can sustain them
2.1a Cells Are Small and Are Visualized Using a Microscope
All forms of life grouped into three domains:1) Bacteria2) Archaea3) Eukarya
prokaryotes no longer grouped bacteria & archaea as one à not evolutionarily related
cells vary in size but are all organized according to the same basic plan & all have structures that perform similar activities
cells are small bc the volume of a cell determines the amount of chemical activity that can take place within it, whereas the surface area determines the amount of substances that can be exchanged between the inside of the cell and the outside environment; if too big à takes long for nutrients to get where they need to go
can have extensions, microvilli, that increase SA à better absorption
2.1b Cells Have a DNAContaining Central Region That Is Surrounded by Cytoplasm
cells are bounded by the plasma membrane= bilayer of lipids w/ embedded protein molecules; hydrophobic barrier to the passage of watersoluble substances
central region of all cells contains DNA molecules hereditary information organized in the form of genes= segments of DNA that
code for individual proteins central core has proteins that help maintain the DNA structure & enzymes that
duplicate DNA & copy its information into RNA
cytoplasm= parts of the cell between the PM & central region
organelles= small, organized structures important for cell function
cytosol= aqueous solution containing ions & various organic molecules
cytoskeleton=proteinbased framework of filamentous structures that helps maintain proper cell shape & plays key roles in cell division & chromosome segregation from cell generation to cell generation thought to be specific to eukaryotes but ALL major eukaryotic cytoskeletal
proteins have functional equivalents in prokaryotes here: synthesis & assembly of most of the molecules required for growth &
reproduction & conversion of chemical & light energy into forms that can be used by cells
conducts stimulatory signals from the outside to the cell interior & carries out chemical reactions that respond to these signals
2.1c Cells Occur in Prokaryotic and Eukaryotic Forms, Each with Distinctive Structures and Organization
Two types of cells:1) Prokaryotic2) Eukaryotic
Prokaryotic cell à lacks a nucleus nucleoid= DNAcontaining central region à has no boundary membrane
separating it from the cytoplasm
Eukaryotic cell à DNA contained within a membranebound compartment called the nucleus
cytoplasm contains extensive membrane systems that form organelles w/ their own distinct environments & specialized functions
plasma membrane surrounds eukaryotic cells as the outer limit of the cytoplasm
2.2 Prokaryotic Cells
most relatively small à much smaller than eukaryotic spherical, rodlike & spiral= most common shapes
Escerichia coli (E.coli) à in intestine model organism rodlike
• genetic material of archaea & bacteria= in nucleoid à contains highly folded mass of DNA
• single circular molecule à the DNA= karyotic chromosome• DNA encodes info for proteins à copied into mRNA• small, roughly spherical particles in the chromosome= ribosomes à use the info in
mRNA to assemble amino acids into proteins consist of a large & small subunits formed from rRNA & protein molecules
• each prokaryotic ribosome contains three types of rRNA & 50+ proteins
cell wall à provides rigidity to prokaryotic cells & w/ capsule, protects the cell from physical damage some contain à glycocalyx à polysaccharide sugar coating; helps protect prokaryotic cell from physical damage & desiccation may enable a cell to attach to a surface either slime layer (loosely associated w/ cells) or capsule (gelatinous & more
firmly attached to cells)
Plasma membrane functions in bacteria & archaea: transport contains most of the molecular systems that metabolize food molecules into the
chemical energy of ATP
most cellular functions occur either in the plasma membrane or in the cytoplasm prokaryotic cytoskeletons play important roles in creating & maintaining the
proper shape of cells & for certain bacteria, in determining the polarity of the cells most bacteria & archaeans can move through liquids & across wet surfaces by
flagella bacterial flagellum à helically shaped; rotates in a socket in the PM & cell wall to
push the cell through a liquid medium some bacteria & archaea have hairlike shafts of protein called pili à attaches the
cell to surfaces or other cells
2.3 Eukaryotic CellsFour major groups:1) protists2) fungi3) animals4) plants
2.3a Eukaryotic Cells Have a True Nucleus and Cytoplasmic Organelles Enclosed within a Plasma Membrane
all have a true nucleus enclosed by membranes cytosol à participates in energy metabolism & molecular synthesis & performs
specialized functions in support & motility PM carries out functions via embedded proteins some proteins= carriers, channels, receptors
supportive cell wall surrounds the PM of fungal, plant & many protist cells à extracellular structure
2.3b The Eukaryotic Nucleus Contains Much More DNA Than the Prokaryotic Nucleoid
nucleus separated from the cytoplasm by the nuclear envelope à double membrane
lamins à lines & reinforces the inner surface of the nuclear envelope in animal cells
nuclear pore complex= large structure formed by many types of proteins called nucleoporins à largest protein complex in the cell; exchanges components between the nucleus & cytoplasm & prevents the transport of material not meant to cross the nuclear membrane
nuclear pore à path for the assisted exchange of large molecules cargo à protein or RNA molecule that assists w/ transport nucleoplasm= liquid/semiliquid substance w/in the nucleus most of the space inside the nucleus= filled w/ chromatin= combo of DNA &
proteins most of the hereditary info is distributed among several linear DNA molecules in
the nucleus each individual DNA associated w/ proteins to become eukaryotic chromosome chromatin= any collection of eukaryotic DNA molecules w/ their associated
proteins chromosome= one complete DNA molecule w/ its associated proteins eukaryotic nuclei contain much more DNA than prokaryotic a eukaryotic nucleus also contains 1+ nucleoli à form around the genes coding for
the rRNA molecules of ribosomes w/in the nucleus à info in rRNA genes is copied into rRNA molecules à combine
w/ proteins to form ribosomal subunits à leave nucleoli & exit the nucleus where they join w/ mRNAs to form complete ribosomes
2.3c Eukaryotic Ribosomes Are Either Free in the Cytosol or Attached to Membranes
consists of a large & small subunit larger than prokaryotic contain 4 types of rRNA & 80+ proteins use the information in mRNA to assemble amino acids into proteins some free in cytosol, others attached to membranes proteins that enter the nucleus become a part of chromatin, line the nuclear
envelope (lamins), or remain in solution in the nucleoplasm
2.3d An Endomembrane System Divides the Cytoplasm into Functional and Structural Compartments
endomembrane system= collection of interrelated internal membranous sacs that divide the cell into functional & structural compartmentsFunctions: synthesis & modification of proteins transport of proteins into membranes & organelles or outside the cell synthesis of lipids detoxification of some toxins membranes connected directly or by vesicles à compartments that transfer
substances between parts of the systemComponents: nuclear envelope ER Golgi complex lysosomes vesicles PM
Endoplasmic Reticulum à extensive interconnected network of membranous channels & vesicles called cisternae cisterna formed by a single membrane that surrounds an enclosed membrane
called the ER lumenRough ER à ribosomes stud outer surface proteins made on ribosomes attached to the ER enter the ER lumen à fold into
final form chemical modifications of proteins occur in the lumen most of proteins formed on rough ER à Golgi complex= next outer membrane of nuclear envelope= closely related in structure & function to
the rough ER (connected)Smooth ER à membranes have no ribosomes attached synthesis of lipids contain enzymes that covert drugs, poisons & toxic byproducts of cellular
metabolism into substances that can be tolerated or more easily removed from the body
cells that are highly active in making proteins like pancreatic cells are packed w/ rough ER but little smooth ER
cells that primarily synthesize lipids or break down toxic substances are packed w/ smooth ER but contain little rough ER
Golgi Complex à named after Camillo Golgi consists of a stack of flattened membranous sac (w/o attached ribosomes) called
cisternae separate sacs, not connected like ER cisternae cells that are highly active in secreting proteins have hundreds of complexes near the rough ER membrane, between the ER & the PM RECEIVE proteins that were made in the ER vesicles from ER contact w/ the cis face & release their contents directly into the
cisternal
protein MODIFICATION (i.e. removing amino acids) modified proteins transported w/in the Golgi to the trans face of the complex regulates the movement of several different types of proteins some embedded in PM, others secreted from cell, others placed in lysosomes proteins secreted from the cell are transported to the PM in secretory vesicles à
release their contents to the exterior by exocytosis à secretory vesicle fuses w/ the PM & spills the vesicle contents to the outside
the membrane of a vesicle that fuses w/ the PM becomes part of the PM à used to expand surface of the cell during cell growth
endocytosis à brings molecules into the cell from the exterior; PM forms a pocket à bulges inward & pinches off into the cytoplasm as an endocytic vesicle; once in the cytoplasm, vesicles which contain segments of PM & proteins, are carried to the Golgi complex
Lysosomes à small, membranebound vesicles that contain 30+ hydrolytic enzymes for the digestion of many complex molecules the cell recycles the subunits of these molecules found in animals BUT NOT PLANTS functions of lysosomes in plants carried out by the CENTRAL VACUOLE human cell= about 300 lysosomes formed by budding from the Golgi complex hydrolytic enzymes are synthesized in the rough ER, modified in the lumen of the
ER to identify them as being found in the lumen of the ER to identify them as being bound for a lysosome, transported to the Golgi complex in a vesicle & then packaged in the budding lysosome
pH= 5 à acidic; do not function in the 7.2 pH cytosol can digest food molecules, etc autophagy à digest organelles that are not functioning correctly; membrane
surrounds the defective organelle, forming a large vesicle that fuses with 1+ lysosomes; the organelle is then degraded by the hydrolytic enzymes
play a role in phagocytosis= process in which some types of cells engulf bacteria or other cellular debris to break them down à produces a large vesicle that contains the engulfed materials until lysosomes fuse w/ the vesicle & release the hydrolytic enzymes necessary for degrading them
2.3e Mitochondria Are the Organelles in Which Cellular Respiration Occurs
= membranebound organelles in which cellular respiration occurs
cellular respiration à the process by which energyrich molecules are broken down to water & CO2 by mitochondrial reactions w/ the release of energy
much of the energy released is captured in ATP à generate most of the ATP require oxygen
Enclosed by two membranes: outer mitochondrial membrane à smooth & covers the outside of the organelle inner mitochondrial membrane à expanded by folds called cristae
both membranes surround mitochondrial matrix ATPgenerating reaction occur in the cristae & matrix matrix contains DNA & ribosomes
2.3f The Cytoskeleton Supports and Moves Cell Structures
shape & internal organization of each type of cell is maintained by its cytoskeleton à the interconnected system of protein fibers & tubes that extends throughout the cytoplasm
reinforces the PM & functions in movement, both of structures w/in the cell & of the cell as a whole
most highly developed in animal cells & supports the cytoplasm from the PM to the nuclear envelope
fibers & tubes of cytoskeleton in plants= less prominent; cell wall & central vacuoleCytoskeleton of animal cells contains structural elements of three major types:1) microtubules à largest cytoskeletal elements2) intermediate filaments3) microfilaments à smallest
plants contain the same 3 each cytoskeletal element is assembled from proteins—microtubules from
tubulins, intermediate filaments from intermediate filament proteins, microfilaments from actins
keratins of animal hair, nails, claws à intermediate filament= cytokeratins lamins assembled from intermediate filament
Microtubules à microscopic tubes w/ an outer diameter of about 25 nm & an inner diameter of about 15 nm; function to construct supportive structures vary widely in length wall consists of 13 protein filaments arranged sidebyside filament= linear polymer of tubulin dimers à each w/ an alpha & beta subunit dimers are attached headtotail giving the microtubule polarity change in length by the addition or removal of tubulin dimers many in an animal cell radiate outward from the cell centre/centrosome at the midpoint= 2 short structures called centrioles microtubules that radiate from the centrosome anchor the ER, Golgi complex,
lysosomes, secretory vesicles & at least some mitochondria in position provide tracks along which vesicles move from the cell interior to the PM intermediate filaments add support separate & move chromosomes during cell division, determining the orientation
for growth of the new cell wall during plant cell division, maintaining the shape of animal cells & moving animal cells themselves
motor proteins push against microtubules to move cell motor proteins that walk along microfilaments= myosins & the ones that walk
along microtubules= dyneins & kinesins
Intermediate filaments à fibers intermediate in size between microtubules & microfilaments parallel bundles, interlinked networks found only in MULTICELLULAR ORGANISMS tissue specific in their protein composition structural support
Microfilaments à thin protein fibers that consist of two polymers of actin subunits wound around each other in a long helical spiral polarity; growth & disassembly occur more rapidly at the 1 end than the 2 end occur in almost all eukaryotic cells & involved in structural & locomotor
functions one of the two components of the contractile elements in muscle fibers of
vertebraes involved in the actively flowing motion of cytoplasm called cytoplasmic
streaming à can transport nutrients, proteins & organelles in both plant & animal cells
in cell division à responsible for dividing the cytoplasm
2.3g Flagella Propel Cells, and Cilia Move Materials over the Cell Surface
flagella & cilia= elongated, slender, motile structures that extend from the cell surface
identical in structure except that cilia are usually shorter than flagella & occur on cells in greater #s
whiplike movements of the flagellum propel a cell through a watery medium & cilia move fluids over the cell surface
bundle of microtubules extends from the base of the tip of a flagellum or cilium à circle of 9 double microtubules surrounds a central microtubule
flagella & cilia arise from the centrioles centriole remains the innermost end of a flagellum or cilium when its
development is complete as the basal body of the structure cilia & flagella found in protozoa & algae in humans à cilia cover the surfaces of cells lining cavities or tubes in some parts
of the body
2.4 Specialized Structures of Plant Cells
2.4a Chloroplasts Are Biochemical Factories Powered by Sunlight
sites of photosynthesis in plant cells; members of a family of plant organelles called plastids
other members of the family= amyloplasts & chromoplasts amyloplasts= colourless plastids that store starch; occur in great numbers in the
roots or tubers of some plants
chromoplasts= contain red & yellow pigments & are responsible for the colours of ripening fruits or autumn leaves
all plastids contain DNA genomes & molecular machinery for gene expression & the synthesis of proteins on ribosomes
some proteins w/in plastids are encoded by their genomes, other encoded by nuclear genes & imported into the organelles
chloroplasts surrounded by a double membrane which enclose the stroma stroma à consists of flattened sacs called thylakoids which form grana thylakoid membranes contain molecules that absorb light energy & convert it to
chemical energy in photosynthesis primary molecule absorbing light= chlorophyll à green pigment present in
chloroplasts chloroplast stroma contains DNA & ribosomes
2.4b Central Vacuoles Have Diverse Roles in Storage, Structural Support, and Cell Growth
central vacuoles= large vesicles identified as distinct organelles of plant cells occupies 90%+ of plant cell volume pressure w/in à supports the cells store salts, organic acids, sugars, storage proteins, pigments & in some cells,
waste products, molecules that provide chemical defense tonoplast= membrane that surrounds the central vacuole à contains transport
proteins that move substances into & out of the central vacuole
2.4c Cell Walls Support and Protect Plant Cells
cell walls of plants are extracellular à occur outside the PM provide support to individual cells & contain the pressure from the central vacuole
& protect cells against invading bacteria & fungi consist of cellulose fibers à give tensile strength to walls, embedded in a network
of highly branched carbs cell walls= perforated by minute channels= plasmodesmata 1000100000 plasmodesmata connecting it to abutting cells à lined by PM so that
connected cells essentially all have one continuous surface membrane most also contain a narrow tubelike structure from the smooth ER allow ions & small molecules to move directly from one cell to another through
the cytosol w/o having to penetrate the PM or cell walls cell walls also surround the cells of fungi & algal protists carbs form the major framework of cell walls
3.5 The Eukaryotic Cell and the Rise of Multicellularity
oldest fossils of eukaryotes are about 2.1 billion years old Two major characteristics that distinguish either archaea or bacteria:
1) the separation of DNA and cytoplasm by a nuclear envelope
2) presence in the cytoplasm of membranebound compartments w/ specialized metabolic & synthetic functions
3.5a The Theory of Endosymbiosis Suggests That Mitochondria and Chloroplasts Evolves from Ingested Prokaryotes
in all eukaryotic cells is energytransforming organelles: mitochondria & chloroplasts
mitochondria & chloroplasts are actually descended from freeliving prokaryotic cells
mitochondria are descended from aerobic (w/ oxygen) bacteria chloroplasts are descended from cyanobacteria endosymbiosis à prokaryotic ancestors of modern mitochondria & chloroplasts
were engulfed by larger prokaryotic cells à advantageous relationship called symbiosis
over time the host cell & endosymbionts became inseparable parts of the same organism
3.5b Several Lines of Evidence Support the Theory of Endosymbiosis
*Six lines of evidence suggest that these energytransducing organelles do not have distinctly prokaryotic characteristics that are not found in other eukaryotic organelles:
1. Morphology à the form or shape of both mitochondria & chloroplasts is similar to that of bacteria & archaea
2. Reproduction à a cell cannot synthesize a mitochondrion or chloroplast à only derived from preexisting mitochondria & chloroplasts
both chloroplasts & mitochondria divide by binary fission3. Genetic information à both mitochondria & chloroplast contain their own
DNA as w/ bacteria & archaea, the DNA molecule in mitochondria & chloroplast is
circular, while the DNA molecules in the nucleus are linear4. Transcription and translation à both chloroplasts & mitochondria contain a
complete transcription & translation machinery the ribosomes of mitochondria & chloroplasts are very similar to the type found in
bacteria5. Electron transport à both mitochondria & chloroplasts have electron
transport chains (ETCs) used to generate chemical energy the ETCs of bacteria & archae are found in the PM & for such cells, swallowed
up by endosymbiosis, this membrane would be found inside the membrane of the endocytic vesicle à yep6. Sequence analysis à chloroplasts ribosomal RNA is most similar to that of
cyanobacteria mitochondrial ribosomal RNA is most similar to that of proteobacteria
*only plants & algae contain both mitochondria & chloroplasts à the event leading to the evolution of mitochondria occurred first once eukaryotic cells w/ the ability for aerobic respiration developed, some of these became photosynthetic after taking up cyanobacteria, evolving into the plants & algae today
3.5c Horizontal Gene Transfer Followed Endosymbiosis
genome= the complete complement of an organism’s genetic material
a typical bacterium has a genome that contains 3000 proteincoding genes mitochondria & chloroplasts do not have roughly the same number of genes human mitochondrial genome= 37 genes & the chloroplast genome of the green
alga after endosymbiosis à the early eukaryotic cell would have contained at least 2 or
3 compartments—each with their own genome functioning independently à each coding proteins required for their structure & function
this view ^ contrasts strongly w/ the modern eukaryotic cell à function of the cell is highly integratedTwo major processes led to this integration: 1) some of the genes that were within the protomitochondrion or
protochloroplast were lost2) many of the genes within the protomitochondria & protochloroplast were
relocated to the nucleus à Horizontal Gene Transfer (HGT) was not a change in gene function, just location HGT does not only pertain to endosymbiotic gene transfer but to any movement
of genes between organisms other than to offspring following transcription in the nucleus & translation on cytosolic ribosomes,
proteins destined for the chloroplast or mitochondrion need to be correctly sorted & imported into these energytransducing organelles, where they are trafficked to the correct location
3.5d The Endomembrane System May Be Derived from the Plasma Membrane
endomembrane system= a collection of internal membranes that divide the cell into structural & functional regions ER, Golgi complex, nuclear envelope most widely held hypothesis= in cell lines leading from prokaryotic cells to
eukaryotes, pockets of the PM may have extended inward & surrounded the nuclear region à some membranes fused around the DNA forming the nuclear envelope, which defines the nucleus
remaining membranes formed vesicles in the cytoplasm that gave rise to the ER & Golgi complex
3.5e Solving an Energy Crisis May Have Led to Eukaryotes
much more bacteria & archaea than eukaryotes archeae & bacteria show remarkable biochemical flexibility à being able to use an
assortment of molecules as sources of energy & carbon & thrive in harsh environments uninhabitable to eukaryotes
prokaryotic cells lack complexity of eukaryotes reason that bacteria & archaea have remained very simple= increased complexity
requires increased energy & while eukaryotic cells can generate huge amounts of it, prokaryotic cells cannot
mitochondria generate much greater amounts of ATP from the breakdown of organic molecules than pathways of anaerobic metabolism
while aerobic bacterium relies on its PM, a typical eukaryotic cell contains hundreds of mitochondria, each having a huge internal membrane SA dedicated to generating ATP
ability of early eukaryotes to generate more ATP à cells could become larger & more complex
3.5f The Evolution of Multicellular Eukaryotes Led to Increased Specialization
evidence of multicellular eukaryotes appears in the fossil record starting about 1.2 billion years ago
in the simplest multicellular organisms à all cells are structurally & functionally autonomous à key trait= division of labour
cells were not functionally identical & thus not structurally similar over evolutionary time à this specialization of cell function led to the development
of the specialized tissues & organs that are so clearly evident in larger eukaryotes there is little evidence in the fossil record of the earliest multicellular organisms it is thought that multicellularity arose more than once, most probably
independently along the lineages leading to fungi, plants & animals useful model for the study of multicellularity à green algae à volvocine unlike a true multicellular organism à a cell colony is a group of cells that are all
of one type; there is no specialization in cell structure or function
Chapter 5: Cell Membrane and Signalling
WHY IT MATTERS Cystic fibrosis affects 1/3900 children people w/ CF suffer from a progressive impairment of lung & gastrointestinal
function CF is caused by mutation to a gene that codes for a protein called the cystic
fibrosis transmembrane conductance regulator (CFTR) in normal cells à CTFR acts as a membrane transport protein that pumps chloride
out of the cells that line the lungs & intestinal tract into the covering mucus lining à results in an electrical gradient across the membrane & leads to the movement of sodium ions in the same direction as the chloride
b/c of the high ion concentration, water moves by osmosis out into the mucus lining, keeping it moist à critical to functioning
w/ CF à the Cl channel CFTR does not function properly à result in water being retained w/in cells à buildup of thick mucus that cannot effectively by removed by coughing à obstructs airways, prevent normal breathing, susceptible to bacterial infections
gene therapy needed
5.1 An Overview of the Structure of Membranes
keys to evolution of life à development of the cell/ plasma membrane PM acts as a selectively permeable barrier à allow for the uptake of key nutrients
& elimination of waste products while maintaining a protected environment for cellular processes
development of the internal membranes allowed for compartmentalization of processes & increased complexity
5.1a A Membrane Consists of Proteins in a Fluid of Lipid Molecules fluid mosaic model= model proposes that membranes are not rigid w/ molecules locked into place but rather consist of proteins w/in a mixture of lipid molecules lipid molecules exist in a bilayer less than 10 nm thick lipid molecules vibrate, flex back & forth, spin, move sideways & exchange places w/in the same bilayer half à a million times/second a lipid molecule only RARELY flip flops between two layers mosaic aspect refers to the fact that most membranes contain an assortment of different types of proteins different lipidprotein compositions myelin à used as an insulator= 18% protein & 82% lipid proteins & other components of ½ of the lipid bilayer are different from those that make up the other half of the lipid bilayer à membrane asymmetry
5.1b Experimental Evidence in Support of the Fluid Mosaic Model
Membranes Are Fluid à David Frye & Michael A. Edidin grew human cells & mouse cells separately in tissue culture à able to tag the human or mouse membrane proteins w/ dye molecules: the human proteins were linked to red dye molecules & the mouse proteins were linked to green Frye & Edidin then fused the human & mouse cells à w/in minutes, they found
that the two distinctly coloured proteins began to mix à indicating the mouse & human proteins had moved around in the fused membranes
Membrane Asymmetry à freeze fracture technique in combo w. electron microscopy à block of cells is rapidly frozen by dipping it in liquid nitrogen à the block is fractured by hitting it w/ a microscopically sharp knife edge à fracture often splits bilayers into inner & outer halves, exposing the membrane interior particles on either side of the membrane differ in size number, and shape,
providing evidence that the two sides are distinctly different
5.2 The Lipid Fabric of a Membrane
fabric of all biological membranes= lipid molecules lipid à diverse group of waterinsoluble molecules that includes fats:
phospholipids & steroids many organisms can adjust the types of lipids in the membrane such that
membranes do not become too stiff (viscous) or too fluid (liquid)
5.2a Phospholipids Are the Dominant Lipids in Membranes
lipid bilayer is formed of phospholipids à each consists of a head group attached to two long chains of carbon & hydrogen (hydrocarbon= fatty acid)
head group consists of glycerol linked to one of several types of alcohols or amino acids by a phosphate group
property that all phospholipids share à amphipathic= hydrophobic & hydrophilic regions
fatty acid chain= nonpolar phosphatecontaining head= polar polar= hydrophilic nonpolar= hydrophobic laundry detergents= amphipathic when added to an aqueous solution, phospholipids selfassemble into 1/3
structures—a micelle, liposome or bilayer b/c of hydrophobic effect—the tendency of polar molecule like water to exclude
hydrophobic molecules such as fatty acids à result= aggregation of lipid molecules in structures where the fatty acid tails interact w/ each other & the polar head groups associate w/ water
favoured b/c require the lowest energy state & are most likely to occur over any other arrangement
5.2b Fatty Acid Composition and Temperature Affect Membrane Fluidity
Fluidity influenced by two factors:1) type of fatty acids that make up the lipid molecules2) temperature
fully saturated fatty acids=linear à allows them to pack together lipid molecules w/ 1+ unsaturated fatty acids prevented from packing closely
together because the presence of double bonds introduces kinks in the fatty acid backbone à results= the more unsaturated fatty acids of the lipid molecules, the more fluid the membrane
temp drop= molecular motion of lipid molecules slows down à fluidity lost & phospholipid molecules form a semisolid gel
the more unsaturated a group of lipid molecules, the lower the temperature at which gelling occurs
5.2c Organisms Can Adjust Fatty Acids Composition
temp can inhibit the function of membranebound enzymes I.e. à ETC à if membrane solidifies, electron transport ceases to operate high temp à too fluid à membrane leakage; imbalance of cellular ions most organisms can actively adjust the fatty acid composition of their membranes
so that proper fluidity is maintained over a broad temperature range I.e. à bacteria, archaea, protists & plants= ecotherms unsaturated fatty acids are produced during fatty acid biosynthesis through the
action of a group of enzymes called desaturases all fatty acids are initially synthesized as fully saturated molecules w/o any double
bonds à desaturases catalyze a reaction that removes two hydrogen atoms from carbon atoms & introduces a double bond
denaturase abundance is regulated at the level of gene transcription à results in changes to desaturase transcription (mRNA) abundance
as growth temp decreases, desturase transcript abundance goes up à increase in synthesis of the desaturase enzyme
higher amounts of desaturase à increase in the abundance of unsaturated fatty acids
by regulating desaturase abundance, many organisms can closely regulate the amount of unsaturated fatty acids that get incorporated into membranes & thereby maintain proper membrane fluidity
sterols also influence membrane fluidity à cholesterol à act as membrane buffer: at high temps à help restrain the movement lipid molecules; at low temps à disrupt fatty acids from associating by occupying space between lipid molecules à slows the transition to the nonfluid gel state
5.3 Membrane ProteinsTwo major types of proteins are associated w/ membranes:1) integral2) peripheral
5.3a The Key Functions of Membrane Proteins
Membrane proteins separated into four major functional categories:1) Transport à channel or carrier2) Enzymatic Activity à # of enzymes= membrane proteins (ETC)3) Signal Transduction à receptor proteins4) Attachment/recognition
5.3b Integral Membrane Proteins Interact with the Membrane Hydrophobic Core
integral membrane proteins= proteins that are embedded in the phospholipid bilayer
transmembrane proteins= a subset of integral membrane proteins that transverse the entire lipid bilayer
transmembrane proteins have domains that differ markedly in polarity b/c they need to interact w/ the hydrophobic & hydrophilic side
the domain that ineracts w/ the lipid bilayer à predominantly nonpolar amino acids that collectively form a type of secondary structure à alpha helix
the portions of a transmembrane protein that are exposed on either side of the membrane are composed of primarily polar amino acids
simple to determine a transmembrane protein à stretches of primarily nonpolar amino acids à 1720 à peptide length needed to span the lipid bilayer
most transmembrane proteins span the membrane more than once I.e. à if a protein has three distinct regions of predominantly nonpolar amino acids
linked by regions that are dominated by polar & charged amino acids à these polar amino acids are found in the portions of the protein that are exposed to the aqueous environment on either side of the membrane
5.3c Peripheral Membrane Proteins Interact with the Membrane Hydrophilic Surface
peripheral membrane proteins= positioned on the surface of a membrane & do not interact w/ the hydrophobic core of the membrane held to membrane surfaces by noncovalent bonds—hydrogen bonds & ionic
bonds—by interacting w/ the exposed portions of integral proteins as well as directly w/ membrane lipid molecules
many found on the cytoplasmic side of the PM & form part of the cytoskeleton key enzymes involved in resp & photosynthetic ETC= peripheral proteins do not interact w/ the hydrophobic core of the membrane à made up of a mixture
of polar & nonpolar amino acids
5.4 Passive Membrane Transport hydrophobic nature of membranes severely restricts the free movement of many
molecules into & out of cells & from one compartment to another ions, charged molecules & macromolecules, do not readily move across
membranes
5.4a Passive Transport Is Based on Diffusion
passive transport= the movement of substances across a membrane w/o the need to expend chemical energy like ATP
diffusion= the net movement of a substance from a region of higher concentration to a region of lower concentration à drives passive transport
diffusion= the primary mechanism of solute movement w/in a cell & between cellular compartments separated by a membrane
driving force behind diffusion= entropy when molecules are more concentrated in one region of a solution or on one side
of a membrane, the molecules are more ordered & in a state of lower entropy
as diffusion occurs, the entropy (disorder) increases, when the molecules are evenly distributed, entropy is highest
as the distribution proceeds to the state of maximum disorder, the molecules release free energy à can accomplish work
rate of diffusion depends on the concentration difference that exists between two areas or across a membrane
the larger the gradient, the faster the rate of diffusion when diffusing molecules reach equilibrium there is still no movement of
molecules from one space to another, but no net change in concentration
5.4b There Are Two Types of Passive Transport: Simple and Facilitated
Two types of passive transport:1) Simple Diffusion 2) Facilitated Diffusion
simple diffusion= the movement of molecules directly across a membrane w/o the involvement of a transporterRate depends on two factors:1) Molecular size2) Lipid solubility
small nonpolar molecules (O2, CO2)= readily soluble in the hydrophobic interior of a membrane & move rapidly from one side to the other
steroid hormones & many amphipathic can readily transit the lipid bilayer small uncharged molecules (water, glycerol) even though they are polar are still
able to move across the membrane membrane is impermeable to charged molecules (Cl, Na+, phosphate)
facilitated diffusion= the diffusion of molecules across a membrane through the aid of a transporter
transport depends on a concentration gradient across a membrane—when the gradient falls to zero, diffusion stops
5.4c Two Groups of Transport Proteins Carry Out Facilitated Diffusion
Two types of transport proteins:1) Channel proteins2) Carrier proteins both are transmembrane proteins
channel proteins à form hydrophilic pathways in the membrane through which molecules can pass aids the diffusion of molecules by providing an avenue that is shielded from the
hydrophobic core of the bilayer specific ones are involved in the transport of certain ions & water
diffusion of water is facilitated by waterspecific transport proteins called aquaporins à bacteria, plants, humans; very narrow & allows for single file movement of 1 billion water molecules/second
very specific for water & does not allow for the diffusion of ions including protons
positive charges in the centre of the channel à repel the transport of protons
gated channel proteins à found in ALL EUKARYOTES can switch between open, closed & intermediate states à critical to the movement
of most ions (Na, K, Ca, Cl) the gates maybe opened or closed by changes in voltage across the membrane or
by binding signal molecules opening or closing involves changes in the protein’s shape in animals à nerve conduction & control of muscle contraction
carrier proteins à form passageways through the lipid bilayer binds a single specific solute & transports it across the bilayer à uniport transport undergoes conformational changes that progressively move the solute binding site
from one side of the membrane to the other à transporting the solute
many transport proteins display a high degree of substrate specificity I.e. à transporters that carry glucose are unable to transport fructose à allows
various cells & cellular compartments to tightly control what gets in and outTo Experimentally Determine if a Molecule is Transported by Facilitated Diffusion and Not Just Simple Diffusion:
w/ facilitated diffusion à rate of movement across the membrane is much faster than one would predict based just on the chemical structure of the molecule being transported
facilitated diffusion can be saturated in the same way as an enzyme, by substrate; a membrane has a limited number of transporters for a particular molecule à if you measure the rate of transport at increasing concentration differences across a membrane, the rate of transport of a particular molecule reaches a plateau= state when essentially all of the transporters are occupied all the time by substrate
increasing the concentration further has no effect on transport in simple diffusion à the whole membrane surface is the transporter; rate never
reaches a plateau but keeps increasing w/ increasing concentration gradient
5.4d Osmosis Is the Passive Diffusion of Water
osmosis= the diffusion of water molecules across a selectively permeable membrane from a solution of lesser solute concentration to a solutions of greater solute concentration à selectively permeable membrane must allow water molecules to pass but not molecules of the solute
occurs in cells because they contain a solution of proteins & other molecules that are retained in the cytoplasm by a membrane impermeable to them but freely permeable to water
can occur by simple diffusion through the lipid bilayer or be facilitated by aquaporins
movement dictated by solute concentration if the solution surrounding a cell contains dissolved substances at lower
concentrations than in the cell à hypotonic to the cell when a cell is in a hypotonic solution, water ENTERS by osmosis & cell swells;
turgor pressure in plant cells if a solution that surrounds a cell contains solutes at higher concentrations than in
the cell, the outside solution= hypertonic to the cell when a cell is in a hypertonic solution, water LEAVES by osmosis & cell shrinks
5.5 Active Membrane Transport compared to simple diffusion, facilitated diffusion increases the rate of movement of molecules across membranes; this type of transport is limited to movement down a concentration gradient
5.5a Active Transport Requires Energy
active transport= the transport of molecules across a membrane against a concentration gradient, requires the expenditure of energy à usually ATP
25% of a cell’s ATP requirements are for the active transport of molecules concentrates molecules such as sugars & amino acids inside cells & pushes ions
into or out of cellsThree main functions of active transport:1) uptake of essential nutrients from the fluid surrounding cells even when their
concentrations are lower than in cells2) removal of secretory or waste materials from cells or organelles even when the
concentration of those materials is higher outside the cells or organelles3) maintenance of essentially constant intracellular concentrations of H+, Na+, K+,
Ca2+ active transport of ions may contribute to voltage, called membrane potentialTwo classes of active transport:1) Primary2) Secondaryprimary active transport à the same protein that transports a substance also hydrolyses ATP to power the transport directlysecondary active transport à the transport is indirectly driven by ATP à transport proteins use a favourable concentration gradient of ions built up by primary active transport as their energy source to drive the transport of a different molecule both processes depend on membrane transport proteins, are specific & can be
saturated the transport proteins= carrier proteins
5.5b Primary Active Transport Moves Positively Charged Ions
these pumps temporarily bind a phosphate group removed from ATP during the pumping cycles
proton pumps à I.e. à in bacteria, archaea, plants & fungi à generate membrane potential
in animals à keep the pH w/in the organelle low calcium pump à eukaryotes; pushes Ca2+ from the cytoplasm to the cell exterior
& from the cytosol into the vesicles of the ER à Ca2+ concentration is typically high outside cells & inside ER vesicles & low in the cytoplasmic solution à used to regulate cellular activities (microtubule assembly, muscle contraction, etc)
sodiumpotassium pump à located in the PM of ALL ANIMAL CELLS pumps 3 Na+ ions OUT & 2 K+ ions IN à positive charges outside & inside
becomes negative à voltage membrane potential= the voltage across a membrane; about 50 to 200
millivolts (charge inside the cell is negative vs. the outside) electrochemical gradient= an electrical difference on the two sides of the
membrane à store energy that is used for other transport mechanisms
5.5c Secondary Active Transport Moves Both Ions and Organic Materials
the transfer of the solute across the membrane is always coupled w/ the transfer of the ion supplying the driving force
occurs by two mechanisms à symport & antiport symport à the cotransported solute moves through the membrane channel in the
same direction as the driving ion à cotransport (glucose & sugars & amino acids) antiport à driving ion moves through the membrane channel in one direction,
providing energy for the active transport of another molecule in the opposite direction à exchange diffusion (RBCs à chloride ions & bicarbonate ions through a membrane channel)
5.6 Exocytosis and Endocytosis eukaryotic cells import & export large molecules by endocytosis & exocytosis the export of materials by exocytosis primarily carries secretory proteins & some waste materials from the cytoplasm to the cell exterior import by endocytosis may carry proteins or even whole cells from outside into the cytoplasm exocytosis & endocytosis also contribute to the backandforth flow of membranes between the endomembrane system & the PM both require energy; both stop if a cell’s ability to make ATP is inhibited
5.6a Exocytosis Releases Molecules to the Outside by Means of Secretory Vesicles
move into the cytoplasm & contact the PM the vesicle membrane fuses w/ the PM à releasing the vesicle’s contents to the cell
exterior
ALL EUKARYOTIC CELLS secrete material to the outside through EXOCYTOSIS
5.6b Endocytosis Brings Materials into Cells in Endocytic Vesicles
substances trapped in pitlike depression that bulge inward from the PM depression pinches off as an endocytic vesicle in MOST eukaryotic cells by ½ pathways bulkphase endocytosis (pinocytosis) à simpler; extracellular water is taken in w/
any molecules that happen to be in solution in the water; no binding by surface receptor
receptormediated endocytosis à the molecules to be taken in are bound to the outer cell surface by receptor proteins
receptors= integral proteins à recognize & bind only certain molecules from the solution surrounding the cell
after binding their target molecules à receptors collect into a depression in the PM à coated pit b/c of the network of proteins (clathrin) that coat & reinforce the cytoplasmic side
the pits deepen & pinch free of the PM to form endocytic vesicles once in the cytoplasm à an endocytic vesicle rapidly loses its clathrin coat & may
fuse w/ a lysosome enzymes w/in the lysosome digest the contents of the vesicle à breakdown the membrane proteins are recycled to the PM
phagocytosis à cell eating (WBCs, amoeba proteus); begins when surface receptors bind molecules on the substances to be taken in
cytoplasmic lobes extend à surround & engulf the materials à form a pit that pinches off & sinks into the cytoplasm as a large endocytic vesicle
materials are digested w/in the cell & any remaining residues are sequestered permanently into storage vesicles or are expelled from cells as waste by exocytosis
5.7 Role of Membranes in Cell Signalling
5.7a Signal Transduction Links Signals with Downstream Cellular Responses
Steps that link the initial perception of a signal w/ it’s ultimate downstream effects = transduction pathway/cascade:1. Reception à binding of a signal molecule w/ a specific receptor of target cells most receptors found on PM receptors= soluble proteins found in the cytoplasm2. Transduction à process whereby signal reception triggers other changes w/in the
cell necessary to cause the cellular response involves a cascade of reactions that include several different molecules à signalling cascade
3. Response à transducted signal causes a specific cellular response different signalling pathways lead to different downstream responses
5.7b Membrane Surface Receptors
membrane receptors that recognize & bind signal molecules= integral membrane proteins that extend through the entire membrane
signalbinding site of the receptor is the part that extends from the outer membrane surface
fit= similar to an enzymesubstrate interaction à specific so that a particular receptor binds only one type of signal
when a signal molecule binds à the molecular structure of that receptor changes so that it transmits the signal through the PM à activating the cytoplasmic end of the receptor protein
activated receptor initiates the first step in a cascade of events that triggers the cellular response
hundreds of membrane receptors on cells
5.7c Signal Reception Triggers Response Pathways within the Cell
signal molecule does not enter the cell à I.e. à signal molecule produces no response if it is injected directly into the cytoplasm & unrelated molecules that mimic the structure of the normal extracellular signal molecule can trigger or block a full cellular response as long as they can bind to the recognition site of the receptor
common characteristic of signalling molecules= the signal is relayed inside the cell by protein kinases à enzymes that transfer a phosphate group from ATP to 1+ sites on particular proteins
often act in a chain à catalyzing a series of phosphorylation reactions à phosphorylation cascade à to pass along the signal
last protein in the cascade= target protein phosphorylation of a target protein stimulates or inhibits its activity depending on
the protein à brings about the cellular response effects of protein kinases in the signal transduction pathways= balanced or reverse
by protein phosphates à remove phosphate groups from target proteins à most are continuously active in cells
by continually removing the phosphate groups from target proteins à protein phosphates quickly shut off a signal transduction pathway if its signal molecule is no longer bound at the cell surface
another characteristic= amplification à an increase in the magnitude of each step as a signal transduction pathway proceeds; occurs b/c many of the proteins that carry out individual steps in the pathways including the protein kinases are enzymes
the more enzymecatalyzed steps in a response pathway à the greater the amplification
Chapter 4.3 Adenosine Triphosphate Is The Energy Currency of the Cell
4.3a ATP Breakdown Releases Free Energy consists of a five carbon sugar, ribose, linked to the nitrogenous base of adenine & a chain of three phosphate groups adenine= ¼ bases that constitute the monomers of DNA & RNA breakdown in an aqueous environment= hydrolysis à liberates free energy & results in the formation of adenosine diphosphate & the orthophosphate ion (HPO4) à inorganic phosphateATP + H2O à ADP + PiDelta G= 7.3 kcal/mol
High free energy of the hydrolysis of ATP is due to three major factors:1) both products of the hydrolysis reaction carry a negative charge à repulsion
between these ionic products favours hydrolysis2) release of the terminal phosphate allows greater opportunity for hydration & this
is energetically favoured state3) the orthophosphate group can exist in a wide variety of resonance forms release of the orthophosphate increases the disorder of the system the high energy of the hydrolysis is simply due to the large difference in the
usable energy content of the reactants (high) as compared to the products (low)
4.3b Energy Coupling Links the Energy of ATP to Other Molecules
hydrolysis= kinetically slow if ATP were especially reactive in an aqueous solution, it would be difficult to see
how controlled metabolism involving ATP would simply release heat, which is a form of energy that is very difficult for the cell to trap & use to work
the generation of high amounts of heat would kill the cell
energy coupling= the exergonic release of energy when ATP is converted to ADP & Pi is used to drive an endergonic reaction requires enzymebased catalysis à enzyme brings a molecule of ATP & a reactant
molecule into close contact free energy of ATP is moved to the reactant molecule through the transfer of the
terminal phosphate group à reactant molecule becomes more unstable & reactive no heat lost b/c ATP is not actually hydrolyzed during energycoupling reactions hydrolysis prevented b/c the site on the enzyme where the ATP & substrate react
is not accessible to water Pi is not produced during energy coupling à the phosphate group is directly
transferred from ATP to the reactant molecule NH3 added to glutamic acid, an amino acid w/ two amino groups to produce
glutamine à used in the assembly of proteins & donor of nitrogen for other reactions in the cell
glutamic acid + NH3 à glutamine + H2O glutamic acid + ATP à glutamyl phosphate + ADP
glutamyl phosphate + NH3 à glutamine + Pi4.3c Cells Also Couple Reactions to Regenerate ATP
ATP is a renewable resource that is made by recombining ADP & Pi if ATP hydrolysis is an exergonic process, then ATP synthesis from ADP & Pi=
endergonic energy from ATP synthesis comes from the exergonic breakdown of complex
molecules that contain an abundance of free energy continued breakdown & resynthesis of ATP= ATP cycle
Chapter 6: Cellular Respiration
WHY IT MATTERS Rolf Luft studiedà hot all the time, weak & thin à metabolic disorder à cells active
but activity was being dissipated as metabolic heat tissue sample from patient’s skeletal muscles à contained many more
mitochondria than normal & were abnormally shaped & enlarged but little ATP generated à Luft sundrome à defect in one of the complexes of cellular respiration that links electron transport to proton pumping & subsequent ATP generation disorder
6.1 The Chemical Basis of Cellular Respiration cellular respiration= the collection of metabolic reactions w/in cells that breaks
down food molecules to produce ATP the ultimate source of the complex organic molecules that are oxidized in cellular
respiration is photosynthesis a major byproduct of photosynthesis= oxygen
6.1a Food Is Fuel
glucose & gasoline= good fuel molecules b/c they contain an abundance of C—H bonds
an electron that is farther away from the nucleus contains more energy than an electron that is more closely held by the nucleus
as an electron moves closer to the nucleus à loses energy; as it moves away à gains energy
the electrons that form the C—H bond are equidistant from both anatomic nuclei à not strongly held by either à electrons can be easily removed & used to perform work
molecules that contain more oxygen (CO2) contain less potential energy b/c O2 is strongly electronegative à greater force that holds the electrons to the atom à greater the energy required to remove the electrons
explains why, compared to proteins & carbs, fats contain more calories (energy) per unit of weight à almost entirely C—H bonds
6.1b Coupled OxidationReduction Reactions Are Central to Energy Metabolism
potential energy contained in fuel molecules= released when the molecules lose electrons à oxidized
molecule gains electrons à reduced ^ coupled process—one cannot happen w/o the other= redox reactions oxidation à many reactions in which electrons are removed from fuel molecules
involve oxygen as the atom that ACCEPTS the electrons high affinity of O2 for electrons makes it ideal as the terminal electron acceptor of
cellular respiration although many oxidation reactions involve O2, others, including a # involved in
cellular respiration, do not the gain or loss of an electron in a redox reaction is not always complete à in some
redox reactions what changes is the degree to which electrons are shared between two atoms
6.1c Cellular Respiration Is Controlled Combustion
glucose can undergo combustion & burn à releases energy as electrons are transferred to oxygen à reducing it to water & the carbon in glucose is converted to CO2
w/in a cell à the oxidation of glucose occurs through a series of enzymecatalyzed reactions à each w. small activation energy
both exergonic, having the same change in free energy à 686 kcal/mol big difference= if you simply burn glucose à the energy is released as heat &
therefore not available to drive metabolic reactions cellular respiration= controlled combustion à energy of C—H bonds is SLOWLY
released w. energy being transferred to other molecules in cellular resp à oxidation of food molecules occurs in the presence of
dehydrogenases à facilitate the transfer of electrons from food to a molecule that acts as an energy carrier
coenzyme nicotinamide adenine dinucleotide (NAD+) à most common energy carrier
during resp à dehydrogenases remove 2 hydrogen atoms from a substrate molecule & transfer the two electrons & 1 proton to NAD+ à reduces to NADH
6.2 Cellular Respiration: An Overview primary goal= to transform the potential energy found in food molecules into a
form that can be used for metabolic processes, ATP
6.2a Cellular Respiration Can Be Divided into Three Phases
1) Glycolysis à enzymes break down a molecule of glucose into 2 molecules of pyruvate; some ATP & NADH made
2) Pyruvate oxidation and the citric acid cycle à acetyl coenzyme A (acetylCoA) à formed from the oxidation of pyruvate à completely oxidized to carbon dioxide; some ATP & NADH made
3) Oxidative phosphorylation à NADH made by glycolysis & the citric acid cycle is oxidized à the liberated electrons are passed along an ETC until they are transferred to oxygen à producing water
free energy released ETC used to generate a proton gradient across a membrane à used to make ATP
NOT ALL ORGANISMS POSSESS ALL THREE STAGES
6.2b The Mitochondrion Is the Site of Cellular Respiration in Eukaryotes
in archaea & bacteria à glycolysis & CAC= IN CYTOSOL; oxidative phosphorylation= on INTERNAL MEMBRANES
in eukaryotic cells à CAC & oxidative phosphorylation= in mitochondria à largest generator of ATP in the cell
mitochondria composed of two membranes à define two compartments: the intermembrane space (between outer & inner membranes) & the matrix (interior aqueous environment)
6.3 Glycolysis: The Splitting of Glucose
= consists of 10 sequential enzymecatalyzed reactions à lead to the oxidation of the sixcarbon sugar glucose producing two molecules of the threecarbon compound pyruvate the potential energy released in the oxidation leads to the overall synthesis of
NADH & ATP
6.3a Glycolysis Is a Universal and Ancient Metabolic Process
one of the first metabolic pathways studied & is one of the best understood, in terms of enzymes involved
first experiments took place over 100 years ago; were some of the first to show, using the extracts from yeast cells, that one could study biological reactions in an isolated, cellfree systemMost fundamental & ancient of all metabolic pathways. Proof:1) universal à found in all three domains of life—archaea, bacteria, eukarya2) does not depend on the presence of O23) occurs in the cytosol of all cells using soluble enzymes à does not require more sophisticated ETCs & internal membrane systems to function
6.3b Glycolysis Includes EnergyRequiring and EnergyReleasing Steps
Three major concepts:1) Energy investment followed by payoff à 2 distinct phases: an initial 5step energy investment followed by a 5step energy payoff; two molecules of ATP are consumed as glucose & fructose6phosphate become phosphorylated à 4 ATP & 2 NADH molecules are produced during the energy payoff phase
2) No carbon is lost à glucose to 2 molecules of pyruvate à no carbon lost; since glucose has been oxidized, the potential energy in 2 molecules of pyruvate is less than that of one molecule of glucose3) ATP is generated by substratelevel phosphorylation à ATP generated by substratelevel phosphorylation à involves the transfer of a phosphate group from a highenergy substrate molecule to ADP à producing ATP; mediated by a specific enzyme; the mode of ATP synthesis used in the CAC
6.4 Pyruvate Oxidation and the Citric Acid Cycle the 2 pyruvate molecules still contain usable free energy the extraction of the remaining free energy in pyruvate & the trapping of this energy in the form of ATP & electron carriers (NADH) are the goals
6.4a Pyruvate Oxidation Links Glycolysis and the Citric Acid Cycle
pyruvate made during glycolysis must pass through the outer & inner mitochondrial membrane à via large pores in outer membrane & pyruvatespecific carriers in inner
once in matrix à converted to acetylCoA via pyruvate oxidation à starts w/ a decarboxylation reaction à carboxyl (COO) group of pyruvate is lost as CO2 à followed by oxidation of the remaining two carbon molecules à make acetate
leads to the transfer of two electrons & a proton to NAD à NADH acetyl group reacts w/ coenzyme A (CoA) à acetylCoA
6.4b The Citric Acid Cycle Oxidizes Acetyl Groups to Carbon Dioxide
citric acid cycle= 8 enzymecatalyzed reactions: 7= soluble enzymes in the mitochondrial matrix & 1 enzyme is bound to the matrix side of the inner mitochondrial membrane; stage of respiration where the remaining carbon atoms that were originally in glucose @ the start of glycolysis are converted into CO2
reactions result in the oxidization of acetyl groups to CO2 accompanied by the synthesis of ATP; NADH & another nucleotidebased molecule (FAD)
1 turn of the CAC à 3 NADH, 1 FADH2, 1 molecule of ATP energy to make these molecules comes from the complete oxidization of 1 acetyl
unit à release of 2 molecules of CO2 the CoA molecule that carried the acetyl group to the CAC is released &
participates again in pyruvate oxidationNet reactants & products:1 acetylCoA+3 NAD+1 FAD+1 ADP+1 Pi+ 2 H2O à 2 CO2+3 NADH+1 FADH2+1 ATP+3 H+1 CoA
all reactants in this equation should be doubled when the CAC is considered as a continuation of glycolysis & pyruvate oxidation
6.5 Oxidative Phosphorylation: Electron Transport and Chemiosmosis after CAC à all the carbon atoms in glucose have been completely oxidized & released as CO2 potential energy now in NADH & FADH2
6.5a The Electron Transport Chain Converts the Potential Energy in NADH and FADH2 into a ProtonMotive Force
ETC in eukaryotes found on the inner mitochondrial membrane à facilitates the transfer of electrons from NADH2 & FADH2 to oxygenFour protein complexes:1) complex I; NADH hydrogenase2) complex II; succinate dehydrogenase3) complex III; cytochrome complex4) complex IV; cytochrome oxidase complex II= single peripheral membrane protein; remaining complexes are composed of multiple proteins electron flow to complexes facilitated by two mobile electron shuttles; Ubiquinone (hydrophobic) à from complexes I & II to complex III; second shuttle= cytochrome c à transfers electrons from complex III to complex IV
6.5b Electrons Move Spontaneously along the Electron Transport Chain
electron transfer NOT BY PROTEINS à by prosthetic groups protein subunits of complex I, III & IV bind a # of prosthetic groups à redox
active cofactors that alternate between reduced & oxidized states as they accept electrons from upstream molecules & donate electrons to downstream molecules
common prosthetic group= heme à component of cytochrome c & many biologically important compounds (haemoglobin)
heme group contains a central redoxactive iron atom that alternates between Fe2+ & Fe3+
during electron transport à 1 of the prosthetic groups of complex I, flavin mononucleotide is reduced by electron donation from NADH on the matrix side of the inner membrane
FMN donates the electron to the Fe/S prosthetic group à donates the electron to ubiquinone à until all electrons are donated to oxygen à reducing it to water
electrons move from high to low energy any single component has a higher affinity for electrons than the preceding carrier
in the chain molecules like NADH contain an abundance of free energy & can be readily
oxidized, but O2 (terminal acceptor) à can be easily reduced
6.5c Chemiosmosis Powers ATP Synthesis by a Proton Gradient
electron transport from NADH or FADH2 to O2 does not actually produce any ATP à electrons passed along a chain until they are donated to oxygen à producing water
energy released during electron transport is used to transport protons across the inner mitochondrial membrane from the matrix to the intermembrane space
H+ becomes much higher in the intermembrane space as compared to the matrix
proton translocation à w/in complexes I & IV à protein components use the energy released from ET for proton pumping & ubiquinone accepts electrons from complexes I & II & picks up protons from the matrix
after carrying à ubiquinone retains a neutral charge by releasing protons into the intermembrane spacePotential energy possessed by a proton gradient is derived from two factors:1) chemical gradient exists across the membrane b/c the concentration of H+ is not equal on both sidesb/c protons are charged, there is an electrical difference, with the intermembrane compartment more positively charged than the matrix
protonmotive force= the combination of concentration gradient and a voltage difference across the membrane produces stored energy
chemiosmosis= harnessing the protonmotive force to do work first proposed as a mechanism to generate ATP energy for chemiosmosis comes from the oxidation of energyrich molecules like
NADH by the ETC; also supplies to the generation of ATP in chloroplasts, where electron transport is driven by light energy
does not only apply to the synthesis of ATP—used to pump substances across membranes & drive the rotation of flagella in bacteria
oxidative phosphorylation= the mode of ATP synthesis that is linked to the oxidation of energyrich molecules by an ETC
relies on the action of à ATP synthase= a large multiprotein complex that spans the inner mitochondrial membrane
6.5d ATP Synthase Is a Molecular Motor
basal unit forms a channel through which H+ can pass freely protonmotive force propels protons in the intermembrane space through the
channel in the enzyme’s basal unit, down their concentration gradient à into the matrix
the binding of individual protons to sites in the headpiece causes it to rotate in a way that catalyzes the formation of ATP from ADP and Pi *ATP is NOT A PRODUCT OF ETC à it is synthesized by chemiosmosis which consumes the proton gradient generated by electron transport
6.5e Electron Transport and Chemiosmosis Can Be Uncoupled
ET & chemiosmotic generation of ATP are separate & distinct processes & not always completely coupled à I.e.: it is possible to have high rates of ET (high oxygen consumption) w/o the synthesis of ATP
uncoupling occurs when mechanisms prevent the formation of the protonmotive force
ionophores à form channels across membranes through which ions can pass à uncouplers à potentially lethal to many organisms b/c they allow for high rates of ET but prevent chemiosmotic ATP synthesis
used to lose weight but overdoses resulted in death when ET is uncoupled from the chemiosmotic synthesis of ATP à the free energy
released during ET is not conserved by the establishment of protonmotive force but instead is lost as heat
uncoupling proteins à localized to the inner mitochondrial membrane & form channels through which protons can freely flow à important in newborns, small mammals, etc
6.6 The Efficiency and Regulation of Cellular Respiration
6.6a What Are the ATP Yield and Efficiency of Cellular Respiration
Oxidative phosphorylation: for each NADH oxidized (each pair of electrons down the ETC), 10 H+ pumped into inner membrane space à 2.53.3 molecules of ATP synthesized/NADH oxidized by the ETC
for every NADH/ 3 ATP 2 molecules ATP/FADH2 products of glycolysis= 2 molecules of ATP & 2 molecules of NADH oxidation of the 2 molecules of pyruvate generated by glycolysis results in the
synthesis of 2 NADH CAC à 2 molecules of acetylCoA that are oxidized result in the synthesis of 2
ATP, along w/ 6 NADH & 2 FADH2 (total= 10 NADH & 2 FADH2 that can be oxidized by the ETC)
Total= 34 ATP generated by oxidative phosphorylation + 2 ATP from glycolysis + 2 ATP directly from the CAC à 38 molecules of ATP
maximum is rarely achieved b/c 1) not in eukaryotic cells à 36 ATP b/c of the energy cost of transporting NADH generated by glycolysis into the mitochondrion (1 ATP/NADH= 2)
2) ET & oxidative phosphorylation= rarely completely coupled to each other à even under normal metabolic conditions à inner mitochondrial membrane= somewhat leaky to protons & not all protons pumped across the ET pass back through the ATP synthase
3) the protonmotive force generated by ET is used for other things à can be harnessed to transport pyruvate into the matrix
38% efficiency > a car
6.6b Fats, Proteins, and Carbohydrates Can Be Oxidized by Cellular Respiration
sucrose & other disaccharides are easily broken into monosaccharides (glucose, fructose) à enter glycolysis at early steps
glycogen is broken down & converted by enzymes into glucose6phosphate
triglycerides= major sources of electrons for ATP synthesis à hydrolyzed into glycerol & individual fatty acids à glycerol converted into glyceraldehyde3phosphate before entering glycolysis
proteins are hydrolyzed to amino acids before oxidation à amino group removed & remainder enters the resp pathway
6.6c Respiratory Intermediates Are Utilized for Anabolic Reactions
organic molecules supply cells w/ the ATP required for growth & metabolism organic molecules generated by the resp pathway are the carbon backbones
required to synthesize a range of essential molecules intermediates of glycolysis & CAC= used as the starting substrate for the anabolic
pathways required to synthesize amino acids, fats, pyrimidine & purine bases
6.6d Cellular Respiration Is Controlled by Supply and Demand
rate of cellular resp= rate of oxygen consumption most metabolic pathways are regulated by supply & demand through the process
of feedback inhibition: the end products of the pathway inhibit an enzyme early in the pathway
key enzyme in glycolysis that is a major site of regulation à prosphofructokinase à catalyzes the conversion of fructose 6phosphate to fructose 1,6biphosphate; allosteric enzyme à activity can be adjusted by the binding of certain metabolic activators & inhibitors; ATP & AMP
when ATP levels in the cell are low, ADP & AMP levels are higher & vice versa if excess ATP present in the cytosol à it binds to phosphofructokinase à inhibiting
its action= decrease in concentration of fructose 1,6biphosphate à slows or stops glycolysis & cell resp as a whole
AMP, accumulates when ATO is being consumed—is an allosteric activator of the enzyme
phosphofructokinase activity is also sensitive to the levels of citrate à first product of the CAC à if products of the CAC are in high demand à citrate should not accumulate in the cell
increased citrate concentrations= demand for ATP= low à limited oxygen
6.7 Oxygen and Cellular Respiration constant supply of oxygen required to maintain the high rates of oxidative phosphorylation two mechanisms by which certain cells can oxidize fuel à fermentation & anaerobic respiration
6.7a In Eukaryotic Cells, Low Oxygen Levels Result in Fermentation
after glycolysis à in eukaryotic cells cell resp can continue via fermentation when no oxygen presentTwo types of fermentation:
1) Lactate fermentation2) Alcohol fermentation
lactate fermentation= pyruvate is converted into lactate occurs in many bacteria, some plant tissues, & certain animal tissues (skeletal
muscle) vigorous muscle activity lactate temporarily stores electrons & when the oxygen content returns to normal
levels, the reverse of the reaction regenerates pyruvate & NADH pyruvate can then be used in the 2nd stage of cellular respiration & the NADH
contributes its electron pair to the ET system lactate= also the fermentation product of some bacteria à sour milk, yogurt, dill
pickles
alcohol fermentation= occurs in microorganisms such as yeast pyruvate is oxidized into 2 successive reactions to a molecule of CO2 & a
molecule of ethyl alcohol as NADH is converted to NAD+ yeast cells convert sugar into ethyl alcohol & CO2 à causes dough to rise beer, wine brewing ripe or rotting fruit à can get birds drunk
by consuming the NADH generated by glycolysis, fermentation reactions keep cytosolic NAD+ levels high à required for glycolysis
as long as there is sufficient NAD+ glycolysis will continue to operate & generate ATP
6.7b In Anaerobic Respiration, the Terminal Electron Acceptor Is Not Oxygen
although they lack mitochondria, many bacteria & archaea have resp ETCs that are located on the internal membrane systems derived from the PM
other bacteria & archaea have resp chains that use a molecule other than O2 as a terminal electron acceptor à anaerobic
instead of O2, sulphate, nitrate & ferric ion are commonly used as the terminal electron acceptors
advantage of aerobic resp à the affinity of oxygen for electrons is greater than that of many of the other electron acceptors
6.7c Organisms Differ with Respect to Their Ability to Use Oxygen
many archaea, bacteria & most eukaryotes= strict aerobes à have an absolute requirement for oxygen to survive & are unable to live solely by fermentation
in the absence of O2 à ATP is generated solely by substratelevel phosphorylation during glycolysis: 2 ATP generated/glucose oxidized in contrast, up to 38 ATP in the presence of O2
certain tissues have a huge energy requirement that is only met by constant & high rates of oxidative phosphorylation
facultative anaerobes à can switch between fermentation & full oxidative pathways
E.coli, lactobacillus, S.cerevisiae
strict anaerobes à require an oxygenfree environment to survive; gain ATP from fermentation à bacteria that cause serious diseases
6.7d The Paradox of Aerobic Life Is That Oxygen Is Essential and Toxic
it takes 4 electrons to completely reduce a molecule of O2 to water reactive oxygen species à partially reduced forms of O2 formed when O2 accepts
fewer electrons if ROS levels w/in a cell are excessive, their strong oxidizing nature can result in
the destruction of many biological molecules & can be lethal cannot be avoided b/c most cells contain an abundance O2 & electron rich
molecules aerobic organisms have evolved an antioxidant defence system that include
enzymes & nonenzyme molecules à intercept & inactivate reactive oxygen molecules as they are produced
strict anaerobes die in the presence of oxygen b/c one group lacks superoxide dismutase & catalase à buildup of toxic reactive oxygen species w/in their cells if exposed to O2
inability of second group à linked to oxygen itself inhibiting key metabolic enzymes
Model Research Organisms Escherichia coli Microbiologists have deciphered the complete DNA sequence of the genome of a standard laboratory strand of E. coli (4400 genes). Onethird of the genes are still unidentified. Got its start in laboratory research because of the ease with which it can be grown in cultures. The cells divide about every 20 minutes; a clone of 1 billion cells can be grown in a matter of hours in 10mL of culture medium. E. coli strains can be grown in the laboratory with minimal equipment, requiring little more than culture vessels in an incubator held at 37 degrees Celsius. The study of naturally occurring plasmids and of enzymes that cut DNA at specific sequences resulted in the development of recombinant DNA techniques – procedure to combine DNA from different sources. Cultures are used as factories for production of desired proteins (Example: the human insulin hormone).
Saccharomyces cerevisiae Baker’s or brewers yeast, the first microorganism to have been domesticated by humans. Favourite strains of baker and brewer’s yeast have been kept in continuous cultures for centuries. Its microscopic size and relatively short generation time make it easy and inexpensive to culture in large numbers in the lab. The complete DNA sequence consists of over 12 million base pairs that encode 6000 genes. Genetic engineering studies have determined that many mammal genes can replace yeast genes when introduced to the fungi, confirming their close relationships. Often called eukaryotic E. coli as it has been so important in the studies of eukaryotes. Another yeast has been similarly productive in the studies of genes that control the cell cycle. Drosophila melanogaster Fruit fly Sexlinked genes, sex linkage, and the first chromosomal map were discovered by studying this organism. Induce mutations in the organism produced all of the major principles and conclusions of eukaryotic genetics. It is easy to culture as it is usually grown at 25 degrees Celsius in small bottles stopped with cotton or plastic foam, and filled onethird with a fermenting medium
The several hundred eggs laid by the adult female hatch quickly and become adult flies within 10 days, which are ready to breed in 1012 hours. Males and females can be easily identified. Mutations produce morphological differences in eye color, wing shape, or the numbers and shapes of the bristles. The fruit fly genome was the first to be sequenced. 14000 genes in its 165 million base pair genome. The relationship between the fruit fly and human genes is close. Studied for model diseases. The studies of fruit fly embryonic development was used to understand the development in humans. Caenorhabditis elegans Tiny freeliving nematode – advances in molecular genetics, animal development and neurobiology. Adult is about 1mm long and thrive on culture of E. coli or other bacteria. Completes its life cycle from egg to reproductive adult in three days at room temperature.
Cultures can be kept alive by freezing them in liquid nitrogen. Store new mutants for later research without having to take care of them until then. Anatomically simple: 959 cells (excluding the gonads). Eggs are transparent. 100 million base pairs, 17000 genes on 6 pairs of chromosomes. Highly relevant to larger organisms such as vertebrates, demonstrate similarities to nematodes, fruit flies and mice in genetic control. In some proteins govern important events such as cell death. In molecular signals used for celltocell communication. Arabidopsis thaliana Tiny member of the mustard family. Grows on a few centimeters tall, so little laboratory space is required to house a larger population. Damps soil and basic nutrients, grows easily and rapidly in artificial light. Grows in one month into a mature plant, then flower and reproduce themselves in 3 to 4 weeks. First complete plant genome to be sequenced, 28000 genes on 5 pairs of chromosomes. Genome contains very little repetitive DNA so easy to isolate the genes used to clone the plant. Amplified by bacteria , the genes and their protein products can be sequenced and studied in other ways. Danio rerio The zebrafish is a 3 cm long, freshwater fish. Native to India spread around the world as aquarium fish. Model vertebrate organism for studying the roles of genes in development. Maintained easily in a aquarium with a simple diet. Generation time is relatively long (3 months), a zebrafish produces 200 offspring at a time. Embryonic development in eggs released outside the female, develop quickly take only three days to lay and hatch. Eggs and embryos are transparent. Investigate its genetics, with a particular interest in genes that regulate embryonic development. 2000 genes, 400 hundred of which that influence development. Most mechanisms controlled by the developmental genes resemble their counter parts in humans and other mammals. Mus musculus The mouse: used in developmental genetics, immunology, and cancer. Used for research that would not be practical or ethical on humans. Small size, inexpensive, and easy to maintain in the laboratory. Short generation time mated at 10 weeks old and in 1822 days females gives
birth to 510 offspring, and can be rebred a day after giving birth. The first example of a lethal allele was found in mice, transplanting tissue between different individuals. 500 mutants cause hereditary diseases, immunological defects, and cancer in mammals including humans. Most spectacular results was the production of giant mice by introducing the human growth hormone gene in the line of dwarfed mice. The sequencing of their gene lead to the researchers refining and expanding their use of the gene and the mouse became the model organism for studies of mammalian biology and diseases. Anolis Lizards of the Caribbean Model system of ecology and evolutionary biology since the 1960s. More than 400 known species, most diverse vertebrate genera known. Less than 10 cm long, not including the tail, occur in high densities, easy to collect a lot of data in a little time. Widely distributed throughout the Caribbean. Ectomorph ? a group of species that have similar morphological, behavioural, and ecological characteristics even though they are not closely related within the genus. Named the emorphs after the vegetation they commonly used (ex. Grass anoles).